PhD., Biostatistics

Johns Hopkins Bloomberg School of Public Health

Baltimore, MD, USA

2016 - 2011

• Advisors: Jeffrey T. Leek and Andrew E. Jaffe
• Thesis: Annotation-Agnostic Differential Expression and Binding Analyses.
• Description: The goal was to develop statistical methods and software that enable researchers to differentiate the sources of variation observed in RNA-seq while minimizing the dependance on known annotation. This allows researchers to correct for technological variation and study the biological variation driving their phenotype of interest. We applied these methods to further our understanding of neuropsychiatric disorders using the Lieber Institute for Brain Development human brains collection (> 1000 samples).

B.S., Genomic Sciences

National Autonomous University of Mexico (UNAM)

Cuernavaca, Morelos, Mexico

2009 - 2005

• Grade 9.71/10
• Third generation at LCG-UNAM

H.S.

ITESM Campus Cuernavaca

Cuernavaca, Morelos, Mexico

2005 - 2002

• Grade 97.8/100
• Best high school average ( 200 students): awarded ITESM system 90% scholarship for college studies, declined to join LCG-UNAM.

Jeff Leek lab

Johns Hopkins Bloomberg School of Public Health

Baltimore, MD, USA

2016 - 2011

• Research Assistant

Enrique Morett Lab

IBT-UNAM

Cuernavaca, Morelos, Mexico

2011 - 2009

• Bioinformatician
• Identified transcriptions start sites and transcription units in Escherichia coli and Geobacter sulfurreducens with RNA-seq data. Developed the BacterialTranscription R package.

Guillermo Dávila Lab

CCG-UNAM

Cuernavaca, Morelos, Mexico

2009 - 2007

• Undergrad research assistant
• Determined bacteriophage ecological groups by developing a method based on codon distribution of all phage sequenced genomes. Joint work with Sur Herrera-Paredes.

Roberto Kolter lab

Harvard University

Boston, MA, US

2007

• Undergrad research assistant
• Supervisor: Elizabeth Shank. Carried out screenings to identify bacteria that activate the production of exopolysaccharide through the activation of the gene tasA in Bacillus subtilis.

Andrew Jaffe Lab

Lieber Institute for Brain Development

Baltimore, MD, USA

N/A

• Staff Scientist II
• At LIBD, Dr. Collado-Torres is part of the Data Science team which goals include better understanding and characterizing genomics signatures in the human brain, including DNA methylation and gene expression. Leonardo helps mentor other team members, provides support for LIBD projects and is advancing his academic career as part of Andrew Jaffe’s lab. He is also a co-founder of the LIBD rstats club and CDSB.

Data Science Division Leader

Winter Genomics

Cuernavaca, Morelos, Mexico

2011 - 2009

• Responsible for recruiting and hiring new personnel, overseeing and supervising bioinformaticians, training new employees, writing research reports and presenting them to colleagues, and organizing all scientific projects.
• First scientific staff member at Winter Genomics; Projects completed: - de novo genome assembly simulations,
• assembly and annotation of the phiVC8 bacteriophage genome,
• integrated analysis of more than 20 RNA-seq samples for determination of transcription initiation in Escherichia coli reported in Gama-Castro et al., PMID 21051347,
• de novo assembly of four Escherichia coli strains and lead to Aguilar et al., PMID 22884033; Designed training material for new employees.

Travel awards

BioC2019, BioC2017, BioC2014, useR2013, BioC2011, From Functional Genomics to Systems Biology 2010 and BiocDevelEurope 2010

N/A

2019 - 2010

• Taught a workshop on recount at BioC2017. Taught a workshop on recount at BioC2017, Gave a talk on BacterialTranscription at BiocDevelEurope2010.
• BioC2019 scholarship application

rstudio::conf 2019 diversity award recipient

announcement

N/A

2019

• Scholarship application.

Early Career Clinical Research Symbiont Award

http://researchsymbionts.org

N/A

2019

• For our work on recount2.

National Researcher level 1

announcement

CONACyT, Mexico

2018

rOpenSci Unconf 2018

unconf18 participants and application

N/A

2018

• Worked on pkginspector.

Bioinformatics Peer Prize III

announcement

N/A

2018

• Competition website, and our winning entry.

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

shiny app, R/Bioconductor package, analysis code

N/A

2020

• Kristen E Maynard \(*\), Leonardo Collado-Torres \(*\), Lukas M. Weber, Cedric Uytingco, Brianna K. Barry, Stephen R. Williams, Joseph L. Catallini II, Matthew N. Tran, Zachary Besich, Madhavi Tippani, Jennifer Chew, Yifeng Yin, Joel E. Kleinman, Thomas M. Hyde, Nikhil Rao, Stephanie C. Hicks, Keri Martinowich \(\dagger\), Andrew E Jaffe \(\dagger\). bioRxiv 969931 (2020). doi: 10.1101/2020.02.28.969931
• Co-first author
• Twitter summary

Recounting the FANTOM CAGE–Associated Transcriptome

related code. Used data from recount2 and code from recount.bwtool

N/A

2020 - 2019

• Eddie-Luidy Imada\(^{*}\), Diego Fernando Sanchez\(^{*}\), Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Aleksey Stupnikov, Francisco Lobo-Pereira, Chi-Wai Yip, Kayoko Yasuzawa, Naoto Kondo, Masayoshi Itoh, Harukazu Suzuki, Takeya Kasukawa, Chung-Chau Hon, Michiel JL de Hoon, Jay W Shin, Piero Carninci, Andrew E Jaffe, Jeffrey T Leek, Alexander Favorov, Gloria R Franco, Benjamin Langmead\(\dagger\), Luigi Marchionni\(\dagger\). Recounting the FANTOM Cage Associated Transcriptome. Genome Research (2020) doi: 10.1101/gr.254656 bioRxiv 659490 (2019). doi: 10.1101/659490
• Supporting role: data preparation and advice
• Twitter summary

Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information

Used data from recount2 and code from recount.bwtool

N/A

2020 - 2019

• Sebastian Guelfi\(^{*}\), Karishma D’Sa\(^{*}\), Juan Botía\(^{*}\), Jana Vandrovcova, Regina H. Reynolds, David Zhang, Daniah Trabzuni, Leonardo Collado-Torres, Andrew Thomason, Pedro Quijada Leyton, Sarah A. Gagliano, Mike A. Nalls, International Parkinson’s Disease Genomics Consortium (IPDGC), UK Brain Expression Consortium, Kerrin S. Small, Colin Smith, Adaikalavan Ramasamy, John Hardy, Michael E. Weale\(\dagger\), Mina Ryten\(\dagger\). Regulatory sites for known and novel splicing in human basal ganglia are enriched for disease-relevant information. Nature Communications (2020) doi: 10.1038/s41467-020-14483-x. bioRxiv 591156 (2019). doi: 10.1101/591156
• Supporting role: data preparation and advice
• Twitter summary

Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

Web browser

N/A

2020 - 2018

• Emily E Burke\(^{*}\), Joshua G Chenoweth\(^{*}\), Joo Heon Shin, Leonardo Collado-Torres, Suel Kee Kim, Nicola Micali, Yanhong Wang, Carlo Colantuoni, Richard E Straub, Daniel J Hoeppner, Huei-Ying Chen, Alana Sellers, Kamel Shibbani, Gregory R Hamersky, Marcelo Diaz Bustamante, BaDoi N Phan, William S Ulrich, Cristian Valencia, Amritha Jaishankar, Amanda J Price, Anandita Rajpurohit, Stephen A Semick, Roland Bürli, James C Barrow, Daniel J Hiler, Stephanie C Page, Keri Martinowich, Thomas M Hyde, Joel E Kleinman, Karen F Berman, José A Apud, Alan J Cross, Nick J Brandon, Daniel R Weinberger, Brady J Maher, Ronald DG McKay\(\dagger\), Andrew E Jaffe\(\dagger\). Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs. Nature Communications (2020) doi: 10.1038/s41467-019-14266-z bioRxiv 380758 (2018). doi: 10.1101/380758
• Supporting role: analysis
• Twitter summary

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex

N/A

N/A

2019

• Kira A Perzel Mandell\(^{*}\), Amanda J Price, Richard Wilton, Leonardo Collado-Torres, Ran Tao, Nicholas J Eagles, Alexander S Szalay, Thomas M Hyde, Daniel R Weinberger, Joel E Kleinman, Andrew E Jaffe\(\dagger\). Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex. bioRxiv 823781 (2019). doi: 10.1101/823781
• Supporting role: analysis
• Twitter summary

recount-brain: a curated repository of human brain RNA-seq datasets metadata

shiny app, code

N/A

2019

• Ashkaun Razmara, Shannon E Ellis, Dustin J Sokolowski, Sean Davis, Michael D Wilson, Jeffrey T Leek, Andrew E Jaffe, Leonardo Collado-Torres\(\dagger\). recount-brain: a curated repository of human brain RNA-seq datasets metadata. bioRxiv 618025 (2019). doi: 10.1101/618025
• Corresponding author
• Twitter summary

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation.

shiny web application

N/A

2019 - 2018

• Amanda J. Price\(^{*}\), Leonardo Collado-Torres\(^{*}\), Nikolay A. Ivanov, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E Jaffe\(\dagger\). Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation. Genome Biology 2019. doi: 10.1186/s13059-019-1805-1. bioRxiv 428391 (2018). doi: 10.1101/428391
• Co-first author
• Twitter summary and summary numbertwo

Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia

web browser

N/A

2019 - 2018

• Leonardo Collado-Torres, Emily E Burke, Amy Peterson, JooHeon Shin, Richard E Straub, Anandita Rajpurohit, Stephen A Semick, William S Ulrich, BrainSeq Consortium, Amanda J Price, Cristian Valencia, Ran Tao, Amy Deep-Soboslay, Thomas M Hyde, Joel E Kleinman, Daniel R Weinberger\(\dagger\), Andrew E Jaffe\(\dagger\). Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia. Neuron 2019. doi: 10.1016/j.neuron.2019.05.013 bioRxiv 426213 (2018). doi: 10.1101/426213
• First-author
• Twitter summary

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods.

N/A

N/A

2019 - 2018

• Carrie Wright\(^{*}\), Anandita Rajpurohit\(^{*}\), Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger\(\dagger\), Joo Heon Shin\(\dagger\).Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. BMC Genomics (2019). doi: 10.1186/s12864-019-5870-3. bioRxiv 445437 (2018). doi: 10.1101/445437
• Supporting role
• Twitter summary

Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells.

Used data from recount2.

N/A

2019

• Anil K Madugundu, Chan Hyun Na, Raja Sekhar Nirujogi, Santosh Renuse, Kwang Pyo Kim, Kathleen H. Burns, Christopher Wilks, Ben Langmead, Shannon E. Ellis, Leonardo Collado-Torres, Marc K. Halushka, Min-Sik Kim, Akhilesh Pandey\(\dagger\). Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. Proteomics 2019. doi: 10.1002/pmic.201800315
• Supporting role
• Twitter summary

Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease.

N/A

N/A

2019 - 2018

• Stephen A Semick, Rahul A Bharadwaj, Leonardo Collado-Torres, Ran Tao, Joo Heon Shin, Amy Deep-Soboslay, James R. Weiss, Daniel R Weinberger, Thomas M Hyde, Joel E Kleinman, Andrew E Jaffe\(\dagger\), Venkata S Mattay\(\dagger\). Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease. Acta Neuropathologica 2019. doi: 10.1007/s00401-019-01966-5. bioRxiv 430603 (2018). doi: 10.1101/430603
• Supporting role: analysis
• Twitter summary

Incomplete annotation of OMIM genes is likely to be limiting the diagnostic yield of genetic testing, particularly for neurogenetic disorders.

Used data from recount2 and code from recount.bwtool

N/A

2018

• David Zhang\(^{*}\), Sebastian Guelfi\(^{*}\), Sonia Garcia Ruiz, Beatrice Costa, Regina H Reynolds, Karishma D’Sa, Wenfei Liu, Thomas Courtin, Amy Peterson, Andrew E Jaffe, John Hardy, Juan Botia, Leonardo Collado-Torres, Mina Ryten. Incomplete annotation of OMIM genes is likely to be limiting the diagnostic yield of genetic testing, particularly for neurogenetic disorders. bioRxiv 499103 (2018). doi: 10.1101/499103
• Supervisor role, data generation, overall project advice
• Twitter summary

RNA-seq transcript quantification from reduced-representation data in recount2

Data available from recount2.

N/A

2018

• Fu J, Kammers K, Nellore A, Collado-Torres L, Leek JT, Taub MA. RNA-seq transcript quantification from reduced-representation data in recount2. bioRxiv 247346 (2018). doi: 10.1101/247346
• Supporting role
• Twitter summary

Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses.

N/A

N/A

2018

• Helena Kuri-Magaña, Leonardo Collado-Torres, Andrew E Jaffe, Humberto Valdovinos-Torres, Marbella Ovilla-Muñoz, Juan M Téllez-Sosa, Laura C Bonifaz-Alfonzo, Jesús Martínez-Barnetche. Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses. Frontiers in Immunology 2018. doi: 10.3389/fimmu.2018.02679 bioRxiv 384172 (2018). doi: 10.1101/384172
• Supporting role: data preparation and advice
• Twitter summary

Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome.

N/A

N/A

2018 - 2017

• Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A, Tao R, Huestis MA, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberger DR, Hancock DB, Kleinman JE\(\dagger\), Jaffe AE\(\dagger\). Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome. Molecular Psychiatry 2018. doi: 110.1038/s41380-018-0223-1. bioRxiv 236968 (2017). doi: 10.1101/236968
• Supporting role: analysis
• Twitter summary

Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis.

N/A

N/A

2018 - 2017

• Jaffe AE, Straub R, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-Soboslay A, The BrainSeq Consortium, Cross AJ, Brandon NJ, Leek JT, Hyde TM, Kleinman JE, Weinberger DR. Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. Nat. Neurosci. 2018. doi: 10.1038/s41593-018-0197-y. bioRxiv 124321 (2017). doi: 10.1101/145656
• Supporting role: analysis
• Twitter summary

Improving the value of public RNA-seq expression data by phenotype prediction.

N/A

N/A

2018 - 2017

• Ellis SE, Collado-Torres L, Jaffe AE, Leek JT. Improving the value of public RNA-seq expression data by phenotype prediction. Nucl. Acids Res. 2018. doi: 10.1093/nar/gky102 bioRxiv 145656 (2017). doi: 10.1101/145656
• Supporting role: data preparation and advice
• Twitter summary and this tweet

Accessing over 70,000 human RNA-seq samples with Bioconductor

N/A

N/A

2017

• Collado-Torres L\(\dagger\), Nellore A, Jaffe AE. recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]. F1000Research (2017). doi: 10.12688/f1000research.12223.1. Winning entry for the Bioinformatics Peer Prize III{bioinformatics-peer-prize-iii.thinkable.org}.
• First and corresponding author
• Twitter summary

Altered expression of histamine signaling genes in autism spectrum disorder

N/A

N/A

2017

• Wright C, Shin JH, Rajpurohit A, Deep-Soboslay A, Collado-Torres L, Brandon NJ, Hyde TM, Kleinman JE, Jaffe AE, Cross AJ, Weinberger DR. Altered expression of histamine signaling genes in autism spectrum disorder. Translational Psychiatry 2017. doi: 10.1038/tp.2017.87
• Supporting role: visualization
• Twitter summary

Reproducible RNA-seq analysis using recount2

N/A

N/A

2017 - 2016

• Collado-Torres L\(^{*}\), Nellore A\(^{*}\), Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. Reproducible RNA-seq analysis using recount2 Nature Biotechnology 2017. doi: 10.1038/nbt.3838 bioRxiv 068478 (2016). doi: 10.1101/068478
• Co-first author
• Twitter summary

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

N/A

N/A

2016

• Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA, Karbhari N, Hansen KD, Langmead B, Leek JT. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. Genome Biology 2016. doi: 10.1186/s13059-016-1118-6. bioRxiv 038224 (2016). doi: 10.1101/038224
• Supporting role: analysis
• bioRxiv tweet

Flexible expressed region analysis for RNA-seq with derfinder.

N/A

N/A

2016

• Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucl. Acids Res. 2016. doi: 10.1093/nar/gkw852 bioRxiv 015370 (2016). doi: 10.1101/015370
• First author
• Twitter summary

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage.

N/A

N/A

2016 - 2015

• Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B. Rail-RNA: Scalable analysis of RNA-seq splicing and coverage. Bioinformatics 2016. doi: 10.1093/bioinformatics/btw575 bioRxiv 019067 (2015). doi: 10.1101/019067
• Supporting role: analysis
• Twitter summary

regionReport: Interactive reports for region-level and feature-level genomic analyses

N/A

N/A

2016 - 2015

• Collado-Torres L, Jaffe AE and Leek JT. regionReport: Interactive reports for region-level and feature-level genomic analyses [version2; referees: 2 approved, 1 approved with reservations]. F1000Research 2016, 4:105. doi: 10.12688/f1000research.6379.2 bioRxiv 016659 (2015). doi: 10.1101/016659
• First author
• Twitter summary

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution.

N/A

N/A

2015

• Jaffe AE, Shin J, Collado-Torres L, Leek JT, et al. Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nat. Neurosci. 2015. doi: 10.1038/nn.3898
• Supporting role: analysis
• Twitter summary

Book chapter: Measurement, Summary, and Methodological Variation in RNA-sequencing

N/A

N/A

2014

• Frazee AC, Collado-Torres L, Jaffe AE, Langmead B, Leek JT. Measurement, Summary, and Methodological Variation in RNA-sequencing in Statistical Analysis of Next Generation Sequencing Data, Springer, 2014, 115-128.

Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus.

N/A

N/A

2011

• Shank EA, Klepac-Ceraj V, Collado-Torres L, Powers GE, Losick R, Kolter R. Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc. Natl. Acad. Sci. U.S.A. 2011 Nov;108(48):E1236–1243. doi: 10.1073/pnas.1103630108
• Supporting role: performed initial experiments
• Twitter summary from 2011? No such thing back then

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

N/A

N/A

2011

• Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J. RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res. 2011 Jan;39(Database issue):D98–105. doi: 10.1093/nar/gkq1110

Bioconductor: author role

spatialLIBD: LIBD Visium spatial transcriptomics human pilot data inspector – (Not Available on 2020-03-02) downloads. GenomicState: data for derfinder analyses – (Not Available on 2020-03-02) downloads. recount: Explore and download data from the recount project – 20751 downloads. derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach – 29644 downloads. derfinderPlot: plotting functions for derfinder results – 12402 downloads. regionReport: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results – 14362 downloads. derfinderHelper: helper functions for derfinder package – 24326 downloads. derfinderData: data for derfinder examples – 2861 downloads.

N/A

2014 - 2020

Mentor role

regutools

Remotely

2020

• Mentored three CDSB alumni while they developed their first R/Bioconductor package.

Bioconductor: contributor role

brainflowprobes, bumphunter, ballgown

N/A

2019 - 2014

Misc R packages

sgejobs: Helper functions for SGE jobs at JHPCE. easyweb: A fast and easy way to build your own website. libdRSE: Custom RSE objects from genomic coordinates on LIBD data. blogdown: contributed the Insert Image and New Post addins. recount.bwtool: Compute coverage matrices from recount quickly using bwtool. jaffelab: commonly used functions by the Jaffe lab. shinycsv: explore a table interactively. enrichedRanges: identify enrichment between two sets of genomic ranges. dots: simplify function calls. fitbitR: visualize your FitBit data. BacterialTranscription: identify TSSs and TUs from RNA-seq data.

N/A

2019 - 2011

shiny web applications

recount-brain: explore recount-brain interactively. wgbsExprs: LIBD WGBS Expression explorer for the methylation and expression associations described by Price et al, 2019. shinycsv: explore a table interactively. recount:: analysis-ready RNA-seq gene and exon counts datasets. MPH capstone TA office hours sign up. Simple mortgage calculator.

N/A

2019 - 2014

• Deployed links: recount-brain, wgbsExprs, recount, shinycsv.

JHU thesis template

GitHub and Overleaf

N/A

2016

Open-source software

Develop and maintain open-source biostatistical software

N/A

2020 - 2011

Peer Review

Biostatistics, Bioinformatics, F1000Research, Nucleic Acids Research, Scientific Reports, Statistical Applications in Genetics and Molecular Biology.

N/A

2020 - 2013

• Full details available through Publons.

Community of Bioinformatics Software Developers (CDSB in Spanish)

Co-founder and Board Member of CDSB which is a community of R and Bioconductor developers in Latin America.

N/A

2020 - 2018

LIBD rstats club

Co-founder and Maintainer of the LIBD rstats club.

Baltimore, MD, USA

2020 - 2018

JHBSPH Student rep

Student representative for the Centennial celebration of the Department of Biostatistics.

Baltimore, MD, USA

2016

JHBSPH Biostatistics Cultural Mixers

Organized Cultural Mixer events for the Department of Biostatistics with Amanda Mejia for raising cultural awareness.

Baltimore, MD, USA

2016 - 2012

Professional memberships

International Society for Computational Biology (2019), American Society of Human Genetics (2015, 2018-2019), American Statistical Association (2015-2017, 2020), ENAR student member (2014-2016), American Public Health Association (2014).

N/A

2014

JHBSPH Genomics for students

Organized the Genomics for Students group (website).

Baltimore, MD, USA

2014 - 2012

IBT-UNAM Genomics Journal Club

Organized a Genomics Journal Club at IBT-UNAM.

Cuernavaca, Morelos, Mexico

2011 - 2009

LCG-UNAM Student rep

Elected class representative for the LCG Academic Committee. Class representative for Administration Unit for Technology Information committee.

Cuernavaca, Morelos, Mexico

2009 - 2008

NNB-UNAM forum launch

Helped start the National Node of Bioinformatics (Mexico) online forum.

Cuernavaca, Morelos, Mexico

2008

CDSB regutools project

Along with Alejandro Reyes, co-mentored Joselyn Chávez, Carmina Barberena-Jonas and Jesus Emiliano Sotelo-Fonseca for the CDSB regutools R/Bioconductor package project.

Remotely

2020 - 2019

Amy Peterson

MPH practicum and MPH capstone advisor.

Baltimore, MD, USA

2018 - 2017

Ashkaun Razmara

MPH practicum and MPH capstone advisor.

Baltimore, MD, USA

2018 - 2017

José Alquicira-Hernández

LCG-UNAM student visiting Jeff Leek’s group.

Baltimore, MD, USA

2015

Winter Genomics mentees

Advised and trained 13 LCG-UNAM students and alumni while working at Winter Genomics: Riveros-McKay F, Vargas-Chávez C, Dulanto-Acevedo V, Romero-Martínez S, Samaniego-Castruita J, Zepeda-Mendoza L, Vargas-Velázquez A, Noé-González M, Soto Jiménez LM, López Moyado I, Medina-Abarca H., Izquierdo-Rangel E, and Berrocal-Quezada NA.

Cuernavaca, Morelos, Mexico

2011 - 2009

LCG-UNAM mentees

Trained 3 LCG-UNAM students to take over the R/Bioconductor course: Reyes-Quiroz A, Moreno-Mayar V, and Reyes-López J.

Cuernavaca, Morelos, Mexico

2009

CDSB

CDSB at LCG-UNAM

Cuernavaca, Morelos, Mexico

2019

• Organizer and instructor for the CDSB 2019 workshop.

Kandahar University Training

Johns Hopkins University

Dubai, UAE

2016

• Instructor for a Biostatistics and Stata workshop for Kandahar University Faculty, organized by Johns Hopkins University (website).

Genomeeting

INMEGEN

Mexico City, CDMX, Mexico

2016

• Instructor for Genomeeting 2016.

Statistical Methods in Public Health

Johns Hopkins Bloomberg School of Public Health

Baltimore, MD, USA

2016 - 2014

• Lead teaching assitant for Statistical Methods in Public Health I and II.

MPH capstone project

Johns Hopkins Bloomberg School of Public Health

Baltimore, MD, USA

2016 - 2014

• Teaching assitant for the MPH capstone projects. 30 min one-on-one consulting sessions (biostatistics, Stata coding).
• Develop and maintain the MPHcapstoneTA shiny application.

Statistical Methods in Public Health

Johns Hopkins Bloomberg School of Public Health

Baltimore, MD, USA

2016 - 2012

• Teaching assitant for Statistical Methods in Public Health I, II, III and IV.

Summer Institute

Johns Hopkins Bloomberg School of Public Health

Baltimore, MD, USA

2015

• Guest lecturer: Introduction to R for Public Health Researchers, Reproducible research module.

Introduction to R for Public Health Researchers

Johns Hopkins Bloomberg School of Public Health

Baltimore, MD, USA

2015

• Teaching assistant

Introduction to R and Biostatistics

LCG-UNAM

Cuernavaca, Morelos, Mexico

2012 - 2011

• Guest lecturer: Seminar 1, Introduction to Bioinformatics course

PDCB-UNAM

CCG-UNAM

Cuernavaca, Morelos, Mexico

2011

• Instructor for the course Introduction to R and Biostatistics for Biomedical Sciences Ph.D. students (website).

PDCB-UNAM

CCG-UNAM

Cuernavaca, Morelos, Mexico

2010

• Instructor for Analysis of High-Throughput Sequencing data with Bioconductor for Biomedical Sciences Ph.D. students (website).

National Bioinformatics Week

Organized by NNB-UNAM at CCG-UNAM

Cuernavaca, Morelos, Mexico

2010

• Instructor of the Introduction to Using Bioconductor for High-Throughput Sequencing Analysis practice lab at the National Bioinformatics Week.

Enrique Morett Lab

IBT-UNAM

Cuernavaca, Morelos, Mexico

2010

• Instructor for the Introduction to R and plotting with R course for Morett’s lab.

Statistical Methods and Analysis of Genomic Data

IBT-UNAM

Cuernavaca, Morelos, Mexico

2010

• Organizer and instructor (website).

Enrique Morett Lab

IBT-UNAM

Cuernavaca, Morelos, Mexico

2009

• Organizer and instructor for the course Introduction to Bioinformatics for Morett’s lab where I taught the Introduction to R and plotting with R module (website)

Seminar III: R/Bioconductor

LCG-UNAM

Cuernavaca, Morelos, Mexico

2009

• Organizer and instructor for an in-depth Bioconductor course (website)

Principles of Statistics

LCG-UNAM

Cuernavaca, Morelos, Mexico

2009

• Basic R (website).

Bioinformatics and Statistics I

LCG-UNAM

Cuernavaca, Morelos, Mexico

2008

• R and Bioconductor overview (website).

rstudio::conf

N/A

San Francisco, CA, USA

2020

• Attended the JavaScript for Shiny users workshop taught by Garrick Aden-Buie.

ASHG

N/A

Houston, TX, USA

2019

• Platform talk: Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia (slides).

Visitors Research Seminar

LIIGH-UNAM

Juriquilla, Qro, Mexico

2019

• Analyzing BrainSeq Phase II and generating the recount-brain resource (slides).

CDSB launch keynote

LCG-UNAM

Cuernavaca, Morelos, Mexico

2019

• Launch of the CDSB 2019 workshop (slides).

BioC

Rockefeller University

New York, NY, USA

2019

• Using the recount2 resource and related tools workshop (slides). Lightning talk on the Community of Bioinformatics Software Developers (slides).
• Also remotely for CONABIO’s bioinformatics course on 2019-10-07 organized by Alicia Mastretta-Yanes.

Biology of Genomes (BoG)

Cold Spring Harbor Laboratory

Cold Spring Harbor, NY, USA

2019

• recount-brain: a curated repository of human brain RNA-seq datasets metadata (poster).

Staff Seminar Series

LIBD

Baltimore, MD, USA

2019

• Analyzing BrainSeq Phase II and generating the recount-brain resource (slides).

rstudio::conf

N/A

Austin, TX, USA

2019

• Attended the Building Tidy Tools workshop by Charlotte and Hadley Wickham.

Pacific Symposium on Biocomputing (PSB)

N/A

Hawaii, HI, USA

2019

• Reproducible RNA-seq analysis with recount2 (slides). Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia (poster).

Joint Genomic Meeting

Johns Hopkins University

Baltimore, MD, USA

2018

• recount-brain: a curated repository of human brain RNA-seq datasets metadata (slides).

Biological Data Science

Cold Spring Harbor Laboratory

Cold Spring Harbor, NY, USA

2018

• Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia (poster).

ASHG

N/A

San Diego, CA, USA

2018

• Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia (poster).

CDSB

Keynote

Remotely

2018

• From learning to using to teaching to developing R (remote presentation) (slides).

SAGES

N/A

Philadelphia, PA, USA

2018

• BrainSeq Phase II: schizophrenia-associated expression differences between the hippocampus and the dorsolateral prefrontal cortex (poster).

LCG-UNAM Remote Talks

LCG-UNAM

Remotely

2018

• Reproducible RNA-seq analysis with recount2 and recount-brain (slides).

SOBP

N/A

New York, NY, USA

2018

• Unique Molecular Correlates of Schizophrenia and Its Genetic Risk in the Hippocampus Compared to Frontal Cortex (slides).

Biology of Genomes (BoG)

Cold Spring Harbor Laboratory

Cold Spring Harbor, NY, USA

2018

• BrainSeq Phase II: Schizophrenia-associated expression differences between the hippocampus and the dorsolateral prefrontal cortex (slides).

rOpenSci Unconf

N/A

Seattle, WA, USA

2018

• Worked on pkginspector.

Journal Club by Dennis Lal

N/A

Remotely

2018

• recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor (slides).

IDIES

Johns Hopkins University

Baltimore, MD, USA

2017

• Getting started with recount2 and accessing it via R (poster).

JSM

N/A

Baltimore, MD, USA

2017

• Guiding principles for interactive graphics based on LIBD data science projects (slides).

Summer Institute

Johns Hopkins University

Baltimore, MD, USA

2017

• Reproducible Research and Bioinformatics (slides).

BioC

Dana-Farber Cancer Institute

Boston, MA, USA

2017

• Reproducible RNA-seq analysis with recount2 workshop (slides).

ICSA

N/A

Chicago, IL, USA

2017

• Reproducible RNA-seq analysis with recount2 (slides).

SOBP

N/A

San Diego, CA, USA

2017

• RNA-seq samples beyond the known transcriptome with derfinder and recount (slides).

Kandahar University Training

Johns Hopkins University

Dubai, UAE

2016

• Introduction at Kandahar University MPH training event (slides).

Genomeeting

INMEGEN

Mexico City, CDMX, Mexico

2016

• recount: facilitando el análisis de miles de muestras de RNA-seq (slides).

SACNAS

N/A

Long Beach, CA, USA

2016

• Using Data Science to Study Human Brain Genomic Measurements (slides).

ENAR

N/A

Austin, TX, USA

2016

• Annotation-agnostic differential expression analysis (slides).

Joint Genomic Meeting

Johns Hopkins University

Baltimore, MD, USA

2015

• dbFinder (slides).

IDIES

Johns Hopkins University

Baltimore, MD, USA

2015

• Annotation-agnostic RNA-seq differential expression analysis software (poster).

Genomics and Bioinformatics Symposium

Johns Hopkins University

Baltimore, MD, USA

2015

• Annotation-agnostic differential expression analysis (slides).

ASHG

N/A

Baltimore, MD, USA

2015

• Annotation-agnostic RNA-seq differential expression analysis software (poster).

Biostatistics Computing Club

Johns Hopkins University

Baltimore, MD, USA

2015

• Easy parallel computing with BiocParallel and HTML reports with knitrBootstrap (slides).

ENAR

N/A

Miami, FL, USA

2015

• Dissecting human brain development at high resolution using RNA-seq (slides).

Joint Genomic Meeting

Johns Hopkins University

Baltimore, MD, USA

2015

• Does mapping simulated RNA-seq reads provide information? (slides).

Jeff Leek lab

Johns Hopkins University

Baltimore, MD, USA

2014

• derfinder tutorial (slides).

is3b: International Summer Symposium on Systems Biology

INMEGEN

Mexico City, CDMX, Mexico

2014

• Developmental regulation of human cortex transcription at base-pair resolution (slides).

BioC

Dana-Farber Cancer Institute

Boston, MA, USA

2014

Biostatistics Computing Club

Johns Hopkins University

Baltimore, MD, USA

2014

• Git for research (slides).

IDIES

Johns Hopkins University

Baltimore, MD, USA

2014

ENAR

N/A

Baltimore, MD, USA

2014

• Fast annotation-agnostic differential expression analysis (poster).

Delta Omega Poster Competition

Johns Hopkins University

Baltimore, MD, USA

2014

• Fast annotation-agnostic differential expression analysis (poster).

LCG-UNAM 10 year anniversary

N/A

Cuernavaca, Morelos, Mexico

2014

• Fast differential expression analysis annotation-agnostic across groups with biological replicates (slides).

Genomics and Bioinformatics Symposium

Johns Hopkins University

Baltimore, MD, USA

2013

• Fast annotation-agnostic differential expression analysis (poster).

Genomics for Students

Johns Hopkins University

Baltimore, MD, USA

2013

• Introduction to ggbio (slides).

Joint Genomic Meeting

Johns Hopkins University

Baltimore, MD, USA

2013

• Fast differential expression analysis annotation-agnostic across groups with biological replicates (slides).

Biostatistics Journal Club

Johns Hopkins University

Baltimore, MD, USA

2013

• Fast differential expression analysis annotation-agnostic across groups with biological replicates (slides).

useR!

N/A

Albacete, Spain

2013

• Differential expression analysis of RNA-seq data at base-pair resolution in multiple biological replicates (slides).

Biostatistics Department Retreat

Johns Hopkins University

Philadelphia, PA, USA

2013

• Differential expression RNA-seq analysis with a large data set from brain samples (poster).

Biostatistics Computing Club

Johns Hopkins University

Baltimore, MD, USA

2013

• Introduction to knitr (slides).

Genomics for Students

Johns Hopkins University

Baltimore, MD, USA

2013

• Introduction to High-Throughput Sequencing and RNA-seq (slides).

Genomics for Students

Johns Hopkins University

Baltimore, MD, USA

2012

• DEXSeq paper discussion (slides).

LCG-UNAM Remote Talks

LCG-UNAM

Remotely

2012

• Introduction to R and Biostatistics (slides).

Biostatistics Computing Club

Johns Hopkins University

Baltimore, MD, USA

2012

• Introducing Git while making your academic webpage (slides).

LCG-UNAM Remote Talks

LCG-UNAM

Remotely

2011

• Introducing Biostatistics to first year LCG students (slides).

BioC

Fred Hutchinson Cancer Research Center

Seattle, WA, USA

2011

Bioconductor Developer Meeting

EMBL

Heidelberg, Germany

2010

• BacterialTranscription: a R package to identify Transcription Start Sites and Transcription Units (slides).

From Functional Genomics to System Biology

EMBL

Heidelberg, Germany

2010

• Global Analysis of Transcription Start Sites and Transcription Units in Bacterial Genomes (poster).

National Bioinformatics Week

Organized by NNB-UNAM at CCG-UNAM

Cuernavaca, Morelos, Mexico

2010

• Introduction to using Bioconductor for High Throughput Sequencing Analysis instructor (slides).

BioC

Fred Hutchinson Cancer Research Center

Seattle, WA, USA

2010

• Global Analysis of Transcription Start Sites and Transcription Units in Bacterial Genomes (poster).

LCG-UNAM Third Generation Symposium

CCG-UNAM

Cuernavaca, Morelos, Mexico

2009

• Bacteriophages: analyzing their diversity (slides).

BioC

Fred Hutchinson Cancer Research Center

Seattle, WA, USA

2009

Course on Oral Communication

CCG-UNAM

Cuernavaca, Morelos, Mexico

2009

• Taught by the master Rafael Popoca.

BioC

Fred Hutchinson Cancer Research Center

Seattle, WA, USA

2008

A Short R/Bioconductor Course

LCG-UNAM

Cuernavaca, Morelos, Mexico

2008

• Taught by James Bullard from UC Berkeley, Ph.D. student in Sandrine Dudoit’s lab at the time.

Boston Bacterial Meeting

N/A

Boston, MA, USA

2007

Department of Microbiology and Molecular Genetics Retreat

Harvard University

Boston, MA, USA

2007

Winter School in Genomics

CCG-UNAM

Cuernavaca, Morelos, Mexico

2006

HUGO

N/A

Kyoto, Japan

2005